test
This project is a part of the larger X-ray tomographic reconstruction toolbox comprised of flexDATA, flexTOMO and flexCALC. flexDATA contains IO routines that were originally developed for the Flex-Ray X-ray CT scanner but can be used for reading and writing data from other types of CT scanners. It provides an interface between a scanner and a GPU-based CT reconstruction ASTRA toolbox. It can be especially helpful when the scanner has many degrees of freedom and the geometry of each scan is defined by a large number of parameters.
It takes a few steps to setup flexDATA on your machine. We recommend that the user installs Anaconda package manager for Python 3.
Simply install with:
conda create -n <your-environment> python=3.6
conda install -c cicwi -c astra-toolbox/label/dev -c conda-forge -c owlas flexdata
To install flexDATA you will need the latest version of the ASTRA toobox (preferably development version). It can be installed via command line with Anaconda:
conda install -c astra-toolbox/label/dev astra-toolbox
To install flexDATA, simply clone this GitHub project. Go to the cloned directory and run PIP installer:
git clone https://github.com/teascavenger/flexdata.git
cd flexdata
pip install -e .
To learn about the functionality of the package check out our examples folder. Examples are separated into blocks that are best to run in Spyder environment step-by-step.
flexDATA is comprised of the following modules:
- io: read / write raw projection stacks (tiffs), parse settings file of the scanner to produce meta data.
- array: some utility functions compatible with large arrays mapped on disk (numpy.memmap)
- scp: wrapper around an SCP client that allows to recursively copy folders across the network
- display:simple display routines for 3D arrays
Typical code:
# Import:
from flexdata import scp
from flexdata import io
# Get files from remote:
scp.ssh_get_path(local_path, remote_path, host, user)
# Read raw projections and flat field images:
proj = io.read_tiffs(path, file_name)
flat = io.read_tiffs(path, file_name)
# Read metadata:
meta = io.read_meta(path, file_type)
# Generate an ASTRA-compatible projection geometry description:
proj_geom = io.astra_proj_geom(meta['geometry'], proj.shape)
- Alexander Kostenko - Initial work
- Allard Handriksen - Packaging and installation
- Jan-Willem Buurlage - Packaging and installation
See also the list of contributors who participated in this project.
Contributions are always welcome. Please submit pull requests against the develop branch.
If you have any issues, questions, or remarks, then please open an issue on GitHub.
This project is licensed under the GNU GENERAL PUBLIC License - see the LICENSE.md file for details
- To Willem Jan Palenstijn for endles advices regarding the use of ASTRA toolbox.